一种异源四倍体恶性杂草叶棘鱼的端粒到端粒基因组组装。

IF 3.9 2区 生物学 Q1 GENETICS & HEREDITY DNA Research Pub Date : 2023-10-01 DOI:10.1093/dnares/dsad023
Mitsuhiko P Sato, Satoshi Iwakami, Kanade Fukunishi, Kai Sugiura, Kentaro Yasuda, Sachiko Isobe, Kenta Shirasawa
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引用次数: 0

摘要

叶棘球蚴是一种在世界各地稻田中发现的异四倍体有害杂草,通常对多种除草剂表现出耐药性。准确的基因组序列对于全面了解该物种特征的遗传基础至关重要。本文介绍了叶栅藻端粒到端粒的基因组序列。使用PacBio高保真长技术构建了跨越1.0Gb的18个染色体序列。在18条染色体中,12个序列完全组装成端粒到端粒和无间隙重叠群,而其余6个序列是在染色体水平上构建的,只有8个间隙。序列被分配到A和B基因组,总长度分别为453和520Mb。重复序列占据了A基因组的42.93%和B基因组的48.47%,尽管在A和B基因组中分别预测了32337和30889个高置信度基因。这表明,在多倍体化以建立四倍体基因组之前,B基因组中经常发生由重复序列积累引起的基因组扩展和基因破坏。高度准确和全面的基因组序列可能是理解有害性状的分子机制和制定有效的杂草控制策略以避免水稻生产中产量损失的里程碑。
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Telomere-to-telomere genome assembly of an allotetraploid pernicious weed, Echinochloa phyllopogon.

Echinochloa phyllopogon is an allotetraploid pernicious weed species found in rice fields worldwide that often exhibit resistance to multiple herbicides. An accurate genome sequence is essential to comprehensively understand the genetic basis underlying the traits of this species. Here, the telomere-to-telomere genome sequence of E. phyllopogon was presented. Eighteen chromosome sequences spanning 1.0 Gb were constructed using the PacBio highly fidelity long technology. Of the 18 chromosomes, 12 sequences were entirely assembled into telomere-to-telomere and gap-free contigs, whereas the remaining six sequences were constructed at the chromosomal level with only eight gaps. The sequences were assigned to the A and B genome with total lengths of 453 and 520 Mb, respectively. Repetitive sequences occupied 42.93% of the A genome and 48.47% of the B genome, although 32,337, and 30,889 high-confidence genes were predicted in the A and B genomes, respectively. This suggested that genome extensions and gene disruptions caused by repeated sequence accumulation often occur in the B genome before polyploidization to establish a tetraploid genome. The highly accurate and comprehensive genome sequence could be a milestone in understanding the molecular mechanisms of the pernicious traits and in developing effective weed control strategies to avoid yield loss in rice production.

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来源期刊
DNA Research
DNA Research 生物-遗传学
CiteScore
6.00
自引率
4.90%
发文量
39
审稿时长
4.5 months
期刊介绍: DNA Research is an internationally peer-reviewed journal which aims at publishing papers of highest quality in broad aspects of DNA and genome-related research. Emphasis will be made on the following subjects: 1) Sequencing and characterization of genomes/important genomic regions, 2) Comprehensive analysis of the functions of genes, gene families and genomes, 3) Techniques and equipments useful for structural and functional analysis of genes, gene families and genomes, 4) Computer algorithms and/or their applications relevant to structural and functional analysis of genes and genomes. The journal also welcomes novel findings in other scientific disciplines related to genomes.
期刊最新文献
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